Search Results (358)

Salmonella Typhimurium is a major zoonotic pathogen, with pigs and chickens serving as key reservoirs for human infection, yet the genomic determinants of its host adaptation remain incompletely understood. This study integrated comparative genomics, genome-wide association studies (GWASs), and interpretable machine learning on 1654 high-quality genomes of swine- and chicken-origin S. Typhimurium isolates to identify host-associated genetic features. Phylogenetic analysis revealed host-preferred lineages and significantly lower genetic diversity within chicken-adapted subpopulations. Meta-analysis identified distinct host-associated profiles of antimicrobial resistance genes (e.g., higher prevalence of floR and bla_TEM-1 in swine) and virulence factors (e.g., enrichment of allB and the yersiniabactin system in chickens). GWASs pinpointed 1878 host-associated genes and multiple SNPs/indels, functionally enriched in metabolism, regulation, and cell processes. A two-stage Random Forest model, built using the most contributory features, accurately discriminated between swine and chicken origins (AUC = 0.974). These findings systematically revealed the genomic signatures of host adaptation in S. Typhimurium, providing a prioritized set of candidate markers for experimental validation. Full article

Legionella pneumophila (L. pneumophila), the primary causative agent of Legionnaires’ disease, is a waterborne bacterial pathogen that poses significant public health concern. This opportunistic pathogen commonly inhabits both natural and man-made water systems, particularly drinking water distribution systems (DWDSs), where it can proliferate and pose a risk to human health. In this study, we evaluated the potential of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for rapid and accurate subtyping of L. pneumophila. Our analysis included 70 L. pneumophila strains collected from the Middle East, representing one of the largest and most comprehensive MALDI-TOF MS-based subtyping of strains from this geographically underrepresented region. These strains, representing three Multi-Locus Variable Number Tandem Repeat Analysis (MLVA-8) genotypic groups (GT4, GT6, and GT15), have been extensively characterized in previous studies for their virulence traits, cytotoxicity patterns, and antimicrobial susceptibility profiles. Our findings revealed distinct genotype-associated spectral signatures with 30 discriminatory m/z peaks (p ≤ 0.005). These markers enabled accurate genotype-level classification, achieving over 85% classification accuracy with a Random Forest model and over 71% accuracy using a Decision Tree algorithm. Importantly, the m/z peak at 5358 was uniquely present in the GT15 strains, whereas m/z 5353 was consistently detected in both GT4 and GT6 isolates, demonstrating the potential of specific mass peaks to serve as reliable genotype markers. Furthermore, GT15 strains consistently formed a separate cluster in both Principal Component Analysis (PCA) and hierarchical analyses, whereas GT4 and GT6 exhibited partial overlap, reflecting their exceptionally high genomic similarity. Full article

Chagas disease (CD), caused by Trypanosoma cruzi, is a neglected tropical illness affecting 6–8 million people in Latin America. Reaching scholarly consensus on the host response to T. cruzi infection remains a significant challenge, primarily due to substantial heterogeneity in outcomes driven by both the choice of animal model and the infecting parasite’s discrete typing unit (DTU). This variability complicates the evaluation and comparison of new therapeutic compounds against existing drugs, namely benznidazole and nifurtimox. This study provides a comprehensive, kinetic, multifaceted characterization of the acute infection using the highly virulent T. cruzi Y strain (TcII) in outbred Swiss mice. Here, crucial infection parameters are presented, including the optimal infective dose, the parasitemia dynamics, tissue damage markers, hematological profiles, cytokine production (Th1/Th2/Th17/Th22), and molecular parasite identification in target organs (heart, colon, esophagus, spleen, and liver) across the span of the infection. The novelty of this study lies in the kinetic integration of these parameters within a defined model; rather than presenting isolated data points, we demonstrate how the biochemical, physiological, and clinical signs and immunological responses, with the resulting organ involvement, evolve and interact over time. To complete the report, a necropsy evaluation was performed at the end of the acute, fatal infection, and it is presented here. This study fulfills a long-standing recommendation from diverse drug discovery groups for the creation of a definitive reference model to standardize preclinical testing for anti-Chagasic agents. Full article

Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy. Full article

Porphyromonas gingivalis (Pg), a keystone pathogen of chronic periodontitis, releases outer membrane vesicles (OMVs) that act as nanoscale vehicles to disseminate virulence factors within periodontal tissues and systemically beyond the oral cavity. Although Pg-OMVs are increasingly recognized as critical mediators of host–pathogen interactions, their effects on the differentiation and function of monocyte–macrophage/osteoclast lineage cells remain unclear. Here, we examined the impact of Pg-OMVs on the differentiation of RAW264.7 monocyte/macrophage-like cells into osteoclasts (OC) and/or macrophages (MΦ) in the presence of receptor activator of nuclear factor-κB ligand (RANKL). OMVs were isolated from Pg W83 and applied to RANKL-primed RAW264.7 cells using three distinct stimulation schedules: (1) simultaneous treatment with Pg-OMVs and RANKL at Day 0; (2) RANKL priming at Day 0 followed by Pg-OMV stimulation at Day 1; and (3) RANKL priming at Day 0 followed by Pg-OMV stimulation at Day 3. In all schedules, cells were cultured for 7 days from the initial RANKL exposure. Remarkably, simultaneous exposure to Pg-OMVs and RANKL (Schedule 1) markedly suppressed osteoclastogenesis (OC-genesis) while promoting M1 macrophage polarization. In contrast, delayed Pg-OMV stimulation of RANKL-primed cells (Schedules 2 and 3) significantly enhanced OC-genesis while reducing M1 polarization. These schedule-dependent effects were consistent with altered expression of osteoclastogenic markers, including dc-stamp, oc-stamp, nfatc1, and acp5. Importantly, a monoclonal antibody against OC-STAMP counteracted the Pg-OMV-induced upregulation of OC-genesis in Schedules 2 and 3. Furthermore, levels of Pg-OMV phagocytosis were inversely correlated with osteoclast formation. Finally, co-stimulation with RANKL and Pg-OMVs (Schedule 1) enhanced macrophage migratory capacity, whereas delayed stimulation with Pg-OMVs (Schedules 2 and 3) did not. Collectively, these findings indicate that Pg-OMVs exert stage-specific effects on the OC/MΦ lineage: stimulation at early stages of RANKL priming suppresses OC-genesis and promotes M1 polarization, whereas stimulation at later stages enhances OC-genesis without inducing M1 differentiation. Thus, Pg-OMVs may critically influence the fate of the OC/MΦ unit in periodontal lesions, contributing to disease progression and tissue destruction. Full article

The historic Rockborn strain of the canine distemper virus was widely used as a vaccine, but its use was discontinued due to safety concerns. Yet, Rockborn-like canine distemper virus strains are still used in some vaccine formulations. Genetic analysis of this strain was previously limited to the H gene, leaving its full evolutionary and pathogenic potential unclear. This study aimed to determine the complete genome sequence of the Rockborn strain to reconstruct its origin, understand its evolution, and provide a reference for improving diagnostics and future research on virulence markers. An amplicon-based sequencing protocol using MinION nanopore technology was employed to determine the complete genome of the Rockborn-46th laboratory strain. The genome was assembled, annotated, and analyzed in comparison with 223 genomes. The complete genome of the Rockborn strain was 15,690 nucleotides in length. Phylogenetic analysis revealed that Rockborn forms a unique lineage with field isolates from a masked civet in China and a dog in the United States. Crucially, a significant recombination event was identified, showing that the Rockborn strain acted as a parental strain, contributing its F and H genes to create mosaic viruses. The full-genome characterization of the Rockborn strain confirms that Rockborn-like viruses persist and actively contribute to the evolution of canine distemper virus through recombination. This finding highlights the inadequacy of single-gene analysis for diagnostics and surveillance, and underscores the necessity of whole-genome sequencing to accurately track the virus epidemiology and evolution. Full article

Introduction: Haemolytic Escherichia coli (E. coli) is commonly associated with enteric disease in pigs and is frequently used as a phenotypic marker for enterotoxigenic E. coli (ETEC). This study aimed to characterise the resistance and virulence profiles of haemolytic E. coli isolated from Colombian pig farms. Methods: A total of 367 faecal samples from sows and pigs across all production stages were collected and analysed for the presence of haemolytic E. coli. Resistance and virulence genes associated with ETEC was detected by multiplex PCR, and antimicrobial susceptibility profiles were determined using broth microdilution and disc diffusion. Results: Haemolytic E. coli were identified in 40.3% of samples (n = 148 non-duplicate isolates), with the highest prevalence observed in growing piglets (47.1%). ETEC occurred in 5.4% of isolates. All isolates exhibited resistance to at least three antimicrobial classes (MDR), with high levels of resistance to tetracycline (98.0%), neomycin (97.3%), chloramphenicol (95.9%), sulfamethoxazole (93.9%), trimethoprim (91.9%), ampicillin (91.9%), nalidixic acid (82.4%), and ciprofloxacin (79.7%). Colistin resistance was observed in 5.4% of isolates, mediated by mcr1 or mcr3, while cefotaxime resistance (8.8%) was extensively associated with blaCTX-M. Conclusions: These findings reveal a concerning burden of MDR E. coli in Colombia’s pig-producing regions and indicate that haemolysis alone is a poor indicator of ETEC. Integrating farm-level antimicrobial use data with genomic analyses will be essential to identify drivers of AMR and guide effective stewardship in the Colombian pig industry. Full article

Bacteriophage therapy, which employs bacterial viruses to selectively eliminate pathogenic bacteria, has re-emerged as a promising strategy in the face of increasing antimicrobial resistance. However, its widespread clinical implementation is constrained by concerns regarding safety, standardisation, and predictable efficacy. In this review, we examine the key role of genomics in transforming phage therapy from an empirical practice into a standardised and personalised modality of contemporary medicine. We describe how whole-genome sequencing (WGS) provides a basis for safety assessment by enabling systematic screening to exclude virulence factors, antibiotic resistance genes, and markers of lysogeny. WGS also facilitates the prediction of therapeutic efficacy and supports more rational phage selection by identifying receptor-binding proteins and characterising bacterial defence systems. In clinical settings, WGS data are increasingly used to monitor the evolution of bacterial populations and to adapt phage cocktails during treatment, thereby supporting personalised, adaptive phage therapy. Looking ahead, further progress is likely to come from integrating synthetic biology and artificial intelligence to engineer phage-based therapeutics with programmable specificity and predictable properties. Together, these developments are shaping a new paradigm of phage therapy as a scientifically grounded, standardised and controlled strategy to treat infections caused by antibiotic-resistant bacteria. Full article

Calonectria ilicicola (anamorph: Cylindrocladium parasiticum) is a globally important soil-borne fungal pathogen, causing Cylindrocladium black rot (CBR) in peanuts (Arachis hypogaea) and red crown rot (RCR) in soybeans (Glycine max), two legume crops central to global food security. Under favorable conditions, these diseases can cause yield losses of 15–50%, with severe epidemics causing substantial economic damage. A defining feature of C. ilicicola is its production of melanized microsclerotia that persist in soil for up to seven years, complicating long-term disease management across major production regions worldwide. The recent spread of RCR into the U.S. Midwest highlights the adaptive potential of the pathogen and underscores the urgency of updated, integrated control strategies. This review synthesizes current knowledge on disease symptoms, pathogen biology, the life cycle, isolation techniques, and molecular diagnostics, with particular emphasis on recent genomic and multiomics advances. These approaches have identified key virulence-associated genes and core pathogenicity factors, providing new insights into host–pathogen interactions and enabling more targeted resistance breeding through marker-assisted selection and the use of wild germplasm. We critically evaluate integrated disease management strategies, including host resistance, chemical and biological control, cultural practices, and physical interventions, highlighting their complementarities and limitations. By integrating classical pathology with emerging molecular and ecological innovations, this review provides a comprehensive background for developing more effective and sustainable management approaches for CBR and RCR. Full article

Objectives: Despite the increasing scientific evidence regarding the application of Cranberries in dentistry, a comprehensive understanding of their potential benefits, active constituents, and mechanisms of action remains lacking. Consequently, this narrative review aims to meticulously analyze and consolidate the existing scientific literature on the utilization of Cranberries for the prevention and treatment of oral diseases. Materials and Methods: Electronic databases (PubMed, Scopus, and Web of Science) were searched up to October 2025. This review included in vitro, in vivo, and clinical research studies. A two-phase selection process was carried out. In phase 1, two reviewers independently screened titles and abstracts to identify potentially eligible studies. In phase 2, the same reviewers performed the full-text assessments of the eligible articles. Results: Among the 93 eligible articles, most assessed Cranberry use in Cariology (n = 28) and Periodontics (n = 26). Biofilm and microbial virulence factors (n = 46) were the most frequently studied topics. Cranberry extract (n = 32) and high-molecular-weight non-dialyzable material (NDM) (n = 23) were the most evaluated Cranberry fractions. Overall, Cranberry-derived compounds were identified as non-toxic and demonstrated promising antimicrobial activity against dental caries-related microorganisms in preclinical studies (n = 20). Regarding periodontal and peri-implant diseases, Cranberry demonstrated host immune modulator effects, counteracting the inflammatory and destructive mechanisms (n = 8). Additionally, Cranberries presented benefits in reducing the inflammation associated with periodontal disease and temporal mandibular joint lesions (n = 1). Regarding dental erosion, Cranberry inhibited dentin erosion (n = 4); however, no effect was observed on enamel lesions (n = 2). As an antioxidant agent, Cranberry showed effectiveness in preventing dental erosion (n = 18). Beyond that, Cranberry neutralized reactive oxygen species generated immediately after dental bleaching, enhancing bond strength (n = 2) and counteracting the oxygen ions formed on the tooth surface following bleaching procedures (n = 3). In osteoclastogenesis assays, A-type proanthocyanidins inhibited bone resorption (n = 1). In osteogenic analysis, preservation of hydroxycarbonate apatite deposition and an increase in early and late osteogenic markers were observed (n = 2). Conclusions: Cranberry bioactive compounds, both individually and synergistically, exhibit substantial potential for diverse applications within dentistry, particularly in the prevention and management of oral and maxillofacial diseases. This review provides insights into the plausible incorporation of Cranberries in contemporary dentistry, offering readers an informed perspective on their potential role. Full article

Background/Objectives: We conducted an untargeted metabolomic study in serum, urine, and fecal water in colorectal cancer (CRC) patients compared to healthy controls. The aim was to define the interactions between metabolites and microbiota. Methods: Effluents were collected before colonoscopy. Metabolites were analyzed using LC-HRMS. Bioinformatics analyses included Limma test, along with spectral house and public databases for annotations. Whole-genome shotgun sequencing was performed on fecal samples. Species–metabolite interactions were calculated using Spearman correlation. Interleukins and inflammatory proteins were measured. Results: Fifty-three patients (11 stage I, 10 stage II, 10 stage III, and 22 stage IV) and twenty controls were included. Derivatives of deoxycholic acid, cholic acid, and fatty acids were lower in serum, while urinary bile acids were higher in stage IV CRC patients (versus controls). Metabolites related to tryptophan and glutamate were found significantly altered in stage IV: upregulation of kynurenine and downregulation of indole pathways. This was linked to increased inflammatory protein and microbial metabolites and to the imbalance between virulent pro-inflammatory bacteria (Escherichia and Desulfovibrio) and symbiotic (Ruminococcus and Bifidobacterium) bacteria. Conclusions: E. coli-related tryptophan catabolism shift is shown through stage IV CRC as compared to controls. As a consequence, tryptophan/kynurenine metabolite may become a promising marker for detecting the failure to immune response during therapy. Full article

Background/Objectives: Accurately diagnosing a periprosthetic joint infection (PJI) represents a challenging and complex task. Especially in the case of low-grade infections, important diagnostic modalities may be inconclusive and synovial markers such as white blood cell count (WBC) and polymorphonuclear percentage (PMN) gain relevance. We therefore aim to assess WBC and PMN in different clinical and microbiological settings. Methods: We performed a retrospective analysis of 115 patients with a diagnosed PJI. WBC and PMN were compared between patients with low- and high-virulent infections, negative and positive histology, symptom duration ≤ 4 weeks and >4 weeks, and positive and negative pathogen detection. Results: Synovial WBC was significantly higher in patients with successful pathogen detection (42.44 [87.0] G/L vs. 16.35 [32.0] G/L; p < 0.01), as was PMN (86.0 [60.0]% vs. 91.0 [89.0]%; p < 0.01). PJIs with high-virulent pathogens showed higher WBC compared to low-virulent pathogens (58.27 [102.0] G/L vs. 27.27 [46.0] G/L; p < 0.01). Patients with onset of symptoms ≤ 4 weeks demonstrated higher WBC (58.27 [112.0] G/L vs. 16.42 [46.0] G/L]; p < 0.01) as well as higher PMN (91.5 [9.0]% vs. 88.0 [20.0]%); p = 0.042). Cases with negative histology showed significantly lower WBC (16.73 [44.0] G/L vs. 42.86 [87.0] G/L; p < 0.01) and lower PMN (86.0 [67.0]% vs. 91.0 [9.0]%; p = 0.036). Conclusions: WBC and PMN show high variability and appear to be influenced by virulence, histology, onset of symptoms, and pathogen detection. Full article

LigiLactobacillus saerimneri (L. sae) has shown considerable promise as a probiotic in recent years, particularly in poultry production. Comprehensive evaluation of its genetic functions, safety profile, and immunogenicity is essential prior to practical application. Our previous study demonstrated that the chicken-derived strain L. sae M-11 colonizes effectively and exhibits a favorable safety profile at adequate dosages. In this study, we further evaluated the potential of L. sae M-11 by analyzing its genetic basis for intestinal adaptation, metabolic features, safety risks, and suitability as a delivery vector. Comparative genomic analysis revealed that L. sae has evolved distinctive genetic features and functional specialization that may facilitate host adaptation. Genomic stability assessments and virulence factor screening confirmed that L. sae M-11 poses no substantial health risks. Furthermore, based on transmembrane protein predictions, the LPQTGE-motif protein was identified as a cell wall anchor in genetically engineered L. sae M-11 using immunoelectron microscopy. Notably, this delivery system selectively activated peripheral blood monocyte-derived dendritic cells (PB-MoDCs) in vitro, as evidenced by the up-regulation of maturation markers (CD83, CD80), pro-inflammatory cytokines (IL-1β, IL-6), Th1-associated IL-12, and the chemokine CXCLi1. However, it exhibited a limited antigen presentation capacity, indicated by low expression levels of CD40, MHCII, DEC205, TNF-α, and IFN-γ. The prospects and challenges associated with the application of L. sae M-11 have been discussed. Overall, these findings support the potential development of L. sae M-11 as a microbial cell factory and mucosal delivery vector. Full article

Platelet concentrates (PCs) are used to treat patients with platelet deficiencies. PCs are stored at 20–24 °C under agitation for up to 7 days to maintain platelet functionality, but these conditions are amenable for proliferation of contaminants such as Staphylococcus aureus, posing a risk for transfusion-transmitted infections. We investigated the contribution of staphylococcal enterotoxins (SEs) type G (SEG) and type H (SEH) to platelet activation, cytokine release, microRNA (miRNA) modulation, and in vivo virulence. PCs were inoculated with wildtype S. aureus CBS2016-05 or SE-deficient mutants (Δseg, Δseh, ΔΔsegh) and monitored during storage. Flow cytometry revealed progressive elevation of platelet activation markers CD62P and Annexin V in contaminated PCs, with significantly higher expression in wildtype compared to SE-mutant strains. Cytokine profiling demonstrated that SEs modulate pro- and anti-inflammatory mediators, notably CCL2, TGF-β1, IFN-γ, and TNF-α, implicating SEG in their regulation. Next-generation sequencing and RT-qPCR validation identified transient induction of immune-related microRNAs miR-98-5p, miR-146a-5p, miR-221-3p, miR-320a-3p, with SE-dependent expression patterns. In a silkworm infection model, wildtype S. aureus-contaminated PCs exhibited significantly higher lethality than SE-deficient strains, confirming toxin-mediated virulence. Collectively, these findings reveal that SEs exacerbate platelet activation and immune dysregulation during storage, enhancing bacterial pathogenicity. This study identifies platelet-derived cytokine and miRNA signatures as potential biomarkers of bacterial contamination and underscores the need to mitigate SE-driven platelet dysfunction to improve transfusion safety. Full article

African swine fever virus (ASFV) is the cause of a severe hemorrhagic disease in domestic pigs and wild boar. Currently, a highly virulent genotype II ASFV is causing massive pig mortality worldwide. In its acute form, the disease is characterized by high fever, a range of non-specific clinical signs and cell death. In this study, we demonstrate a greatly elevated level (>1000-fold) of cell-free DNA (cfDNA), more specifically, fragmented host genomic DNA (gDNA), in serum from both wild boar and domestic pigs infected with a highly virulent genotype II ASFV. Increases were also observed, to a lesser extent, in the serum levels of mitochondrial DNA (between 4- to >500-fold). For comparison, release of the cytoplasmic enzyme, lactate dehydrogenase, which is a commonly used marker for cellular damage, was also found to be elevated in some animals, but with less consistency. These results indicate that gDNA in serum (i.e., cfDNA) can be a useful marker for cell death during infection with highly virulent variants of the virus, and could be a promising biomarker to elucidate the pathogenesis of ASFV infection in both domestic pigs and wild boar in future studies. Full article